The paper studies the influence of geoecological factors on the content of phenolic compounds (PCs) in lichens of the genus Cladonia in the Velsko-Ustyansky and Kholmogorsky tectonic knots (TKs). Lichens were sampled from the test plots (TPs) laid out in the center of the knots and outside the knots (control). The geochemical situation, soil-climatic and environmental conditions in the zone of TKs influence the lichens chemical composition. It is found that the ash content of lichens growing in the center of the TK is 1.8–2.3 times higher than in the control, which indicates a significant accumulation of lithogenic elements in the lichen thallus in the tectonic fault zone. Lichens are exposed to multifactorial adverse effects (increased radiation background and heat flux, electromagnetic radiation, electric and magnetic fields, etc.) in the territory of TKs. This provokes excessive generation of active oxygen radicals and contributes to the rearrangement of lichen metabolism, changing the dynamics of accumulation of PCs and their biosynthesis. The content of the water-insoluble fraction of PCs in lichens was found to increase from the control point to the center of the TK, while the relative share of the water-soluble fraction of PCs in the total composition decreases. This is probably due to an increase in oxidative processes and a decrease in reductive processes in lichens under adverse conditions. The paper shows that the biosynthesis of PCs in lichens is most active in the spring-summer (April and July) vegetation period. The impact of geoecological factors enhances the biosynthesis of secondary metabolites of phenolic nature in lichens in the conditions of the TKs: usnic acid (UA) and atranorin. The content of UA in the composition of the water-insoluble fraction of PCs in lichens growing in the center of the TK is 1.5–1.7 times higher during the spring-summer vegetation period than in lichens growing outside the TK. The quantitative distribution of the water-insoluble fraction of PCs depends on the lichen thallus part and has a gradient character. Their content in the upper growing parts of lichens growing in the center of the TK and in the control is 2 and 1.7 times higher than in the old zones, respectively. Thus, PCs in lichens are active metabolites and their content in thallus can serve as a biomarker of the state of the environment.